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SVMtm specifications

Information


Unique identifier OMICS_07264
Name SVMtm
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Dr. Zheng Yuan <>

Publication for SVMtm

SVMtm in publications

 (9)
PMCID: 4209838
PMID: 25371825
DOI: 10.1155/2014/129849

[…] otherwise., the topology of oatp1b1 was predicted using the online prediction programs topcons [], phobius [], tmpred [], toppred ii [], membrain [], phdhtm [], split 4.0 [], philius [], hmmtop [], svmtm [], conpred ii [], sosui [], tmhmm [], tseg [], pred-tmr [], and memsat3 []. a homology model was generated using the protein homology/analogy recognition engine v 2.0 (phyre2) [], […]

PMCID: 4053335
PMID: 24918783
DOI: 10.1371/journal.pone.0098985

[…] uniprotkb/swiss-prot and hhpred . functional domains were predicted using pfam , and prosite . the putative signal peptide of pa4107 was predicted using tmhmm 1.0 , signalip 4.0 , predisi and svmtm ., pa4107 (efhp) was deleted from the chromosomes of pao1 and frd1 and replaced with the gentamicin omega fragment using the allelic exchange strategy as described previously . the primers used […]

PMCID: 3610235
PMID: 23497205
DOI: 10.1186/1471-2164-14-175

[…] and from the m. hyopneumoniae 7448 and m. hyorhinis hub-1 genomes (nc_007332 and nc_014448 entries, respectively) were analyzed using the default parameters by the following software programs: svmtm transmembrane domain predictor [], tmhmm server v. 2.0 [], scampi [], and psortb []. the first three programs predicted the presence of transmembrane (tm) domains, and the fourth was used […]

PMCID: 3283625
PMID: 22363620
DOI: 10.1371/journal.pone.0031324

[…] a closer inspection of topology predictions revealed that the number of transmembrane domains vary considerably from no transmembrane domain (minnou, phdhtm, s-tmhmm_v0.9, tmhmm_v2, sosuig_v1.1, svmtm_v3, thumbup_v1, tmmod) to one transmembrane domain (memsat_v3, phobius, predtmr_v1, scampi, alom_v2, das-tmfilter, eiconda_v1), two transmembrane domains (tmpred, toppred_v2), and three […]

PMCID: 3182993
PMID: 21980401
DOI: 10.1371/journal.pone.0025228

[…] include zebrafish (danio rerio) and sea squirts (ciona intestinalis and ciona savignyi) which have multiple paralogues., structural predictions using online transmembrane prediction programs (svmtm , tmpred, tmhmm , hmmtop and swissprot) suggest that tmem26 contains between 5 and 8 transmembrane domains, with the most commonly predicted number being 7. the variation between predictions […]


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SVMtm institution(s)
ARC Centre in Bioinformatics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, Australia

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